Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/cwltool/tests/test_provenance.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 import json
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2 import ntpath
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3 import os
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4 import posixpath
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5 import shutil
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6 import sys
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7 import tempfile
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8 from io import open
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9 try:
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10 import cPickle as pickle
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11 except ImportError:
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12 import pickle
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13
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14 from six.moves import urllib
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15
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16 import arcp
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17 import pytest
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18 from rdflib import Graph, Literal, Namespace, URIRef
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19 from rdflib.namespace import DC, DCTERMS, RDF
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20
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21 import bagit
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22 # Module to be tested
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23 from cwltool import load_tool, provenance
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24 from cwltool.main import main
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25 from cwltool.resolver import Path
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26 from cwltool.context import RuntimeContext
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27 from cwltool.stdfsaccess import StdFsAccess
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28
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29 from .util import get_data, needs_docker, temp_dir, working_directory
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30
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31 # RDF namespaces we'll query for later
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32 ORE = Namespace("http://www.openarchives.org/ore/terms/")
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33 PROV = Namespace("http://www.w3.org/ns/prov#")
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34 RO = Namespace("http://purl.org/wf4ever/ro#")
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35 WFDESC = Namespace("http://purl.org/wf4ever/wfdesc#")
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36 WFPROV = Namespace("http://purl.org/wf4ever/wfprov#")
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37 SCHEMA = Namespace("http://schema.org/")
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38 CWLPROV = Namespace("https://w3id.org/cwl/prov#")
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39 OA = Namespace("http://www.w3.org/ns/oa#")
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40
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41
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42 @pytest.fixture
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43 def folder(tmpdir):
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44 directory = str(tmpdir)
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45 if os.environ.get("DEBUG"):
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46 print("%s folder: %s" % (__loader__.fullname, folder))
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47 yield directory
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48
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49 if not os.environ.get("DEBUG"):
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50 shutil.rmtree(directory)
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51
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52
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53 def cwltool(folder, *args):
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54 new_args = ['--provenance', folder]
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55 new_args.extend(args)
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56 # Run within a temporary directory to not pollute git checkout
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57 with temp_dir("cwltool-run") as tmp_dir:
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58 with working_directory(tmp_dir):
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59 status = main(new_args)
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60 assert status == 0, "Failed: cwltool.main(%r)" % (args)
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61
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62 @needs_docker
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63 def test_hello_workflow(folder):
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64 cwltool(folder, get_data('tests/wf/hello-workflow.cwl'), "--usermessage", "Hello workflow")
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65 check_provenance(folder)
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66
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67 @needs_docker
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68 def test_hello_single_tool(folder):
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69 cwltool(folder, get_data('tests/wf/hello_single_tool.cwl'), "--message", "Hello tool")
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70 check_provenance(folder, single_tool=True)
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71
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72 @needs_docker
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73 def test_revsort_workflow(folder):
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74 cwltool(folder, get_data('tests/wf/revsort.cwl'), get_data('tests/wf/revsort-job.json'))
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75 check_output_object(folder)
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76 check_provenance(folder)
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77
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78 @needs_docker
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79 def test_nested_workflow(folder):
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80 cwltool(folder, get_data('tests/wf/nested.cwl'))
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81 check_provenance(folder, nested=True)
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82
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83 @needs_docker
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84 def test_secondary_files_implicit(folder, tmpdir):
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85 file1 = tmpdir.join("foo1.txt")
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86 file1idx = tmpdir.join("foo1.txt.idx")
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87
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88 with open(str(file1), "w", encoding="ascii") as f:
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89 f.write(u"foo")
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90 with open(str(file1idx), "w", encoding="ascii") as f:
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91 f.write(u"bar")
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92
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93 # secondary will be picked up by .idx
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94 cwltool(folder, get_data('tests/wf/sec-wf.cwl'), "--file1", str(file1))
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95 check_provenance(folder, secondary_files=True)
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96 check_secondary_files(folder)
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97
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98 @needs_docker
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99 def test_secondary_files_explicit(folder, tmpdir):
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100 orig_tempdir = tempfile.tempdir
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101 tempfile.tempdir = str(tmpdir)
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102 # Deliberately do NOT have common basename or extension
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103 file1 = tempfile.mktemp("foo")
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104 file1idx = tempfile.mktemp("bar")
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105
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106 with open(file1, "w", encoding="ascii") as f:
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107 f.write(u"foo")
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108 with open(file1idx, "w", encoding="ascii") as f:
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109 f.write(u"bar")
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110
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111 # explicit secondaryFiles
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112 job = {"file1":
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113 {"class": "File",
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114 "path": file1,
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115 "basename": "foo1.txt",
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116 "secondaryFiles": [
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117 {
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118 "class": "File",
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119 "path": file1idx,
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120 "basename": "foo1.txt.idx",
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121 }
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122 ]
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123 }
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124 }
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125 jobJson = tempfile.mktemp("job.json")
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126 with open(jobJson, "wb") as fp:
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127 j = json.dumps(job, ensure_ascii=True)
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128 fp.write(j.encode("ascii"))
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129
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130 cwltool(folder, get_data('tests/wf/sec-wf.cwl'), jobJson)
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131 check_provenance(folder, secondary_files=True)
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132 check_secondary_files(folder)
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133 tempfile.tempdir = orig_tempdir
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134
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135 @needs_docker
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136 def test_secondary_files_output(folder):
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137 # secondary will be picked up by .idx
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138 cwltool(folder, get_data('tests/wf/sec-wf-out.cwl'))
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139 check_provenance(folder, secondary_files=True)
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140 # Skipped, not the same secondary files as above
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141 #self.check_secondary_files()
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142
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143 @needs_docker
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144 def test_directory_workflow(folder, tmpdir):
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145 dir2 = tmpdir.join("dir2")
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146 os.makedirs(str(dir2))
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147 sha1 = {
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148 # Expected hashes of ASCII letters (no linefeed)
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149 # as returned from:
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150 # for x in a b c ; do echo -n $x | sha1sum ; done
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151 "a": "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",
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152 "b": "e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",
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153 "c": "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",
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154 }
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155 for x in u"abc":
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156 # Make test files with predictable hashes
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157 with open(str(dir2.join(x)), "w", encoding="ascii") as f:
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158 f.write(x)
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159
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160 cwltool(folder, get_data('tests/wf/directory.cwl'), "--dir", str(dir2))
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161 check_provenance(folder, directory=True)
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162
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163 # Output should include ls stdout of filenames a b c on each line
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164 file_list = os.path.join(
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165 folder, "data",
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166 # checksum as returned from:
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167 # echo -e "a\nb\nc" | sha1sum
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168 # 3ca69e8d6c234a469d16ac28a4a658c92267c423 -
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169 "3c",
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170 "3ca69e8d6c234a469d16ac28a4a658c92267c423")
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171 assert os.path.isfile(file_list)
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172
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173 # Input files should be captured by hash value,
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174 # even if they were inside a class: Directory
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175 for (l, l_hash) in sha1.items():
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176 prefix = l_hash[:2] # first 2 letters
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177 p = os.path.join(folder, "data", prefix, l_hash)
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178 assert os.path.isfile(p), "Could not find %s as %s" % (l, p)
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179
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180 def check_output_object(base_path):
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181 output_obj = os.path.join(base_path, "workflow", "primary-output.json")
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182 compare_checksum = "sha1$b9214658cc453331b62c2282b772a5c063dbd284"
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183 compare_location = "../data/b9/b9214658cc453331b62c2282b772a5c063dbd284"
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184 with open(output_obj) as fp:
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185 out_json = json.load(fp)
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186 f1 = out_json["sorted_output"]
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187 assert f1["checksum"] == compare_checksum
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188 assert f1["location"] == compare_location
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189
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190
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191 def check_secondary_files(base_path):
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192 foo_data = os.path.join(
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193 base_path, "data",
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194 # checksum as returned from:
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195 # $ echo -n foo | sha1sum
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196 # 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 -
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197 "0b",
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198 "0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33")
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199 bar_data = os.path.join(
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200 base_path, "data", "62", "62cdb7020ff920e5aa642c3d4066950dd1f01f4d")
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201 assert os.path.isfile(foo_data), "Did not capture file.txt 'foo'"
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202 assert os.path.isfile(bar_data), "Did not capture secondary file.txt.idx 'bar"
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203
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204 primary_job = os.path.join(base_path, "workflow", "primary-job.json")
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205 with open(primary_job) as fp:
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206 job_json = json.load(fp)
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207 # TODO: Verify secondaryFile in primary-job.json
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208 f1 = job_json["file1"]
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209 assert f1["location"] == "../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33"
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210 assert f1["basename"] == "foo1.txt"
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211
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212 secondaries = f1["secondaryFiles"]
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213 assert secondaries
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214 f1idx = secondaries[0]
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215 assert f1idx["location"] == "../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d"
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216 assert f1idx["basename"], "foo1.txt.idx"
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217
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218 def check_provenance(base_path, nested=False, single_tool=False, directory=False,
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219 secondary_files=False):
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220 check_folders(base_path)
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221 check_bagit(base_path)
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222 check_ro(base_path, nested=nested)
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223 check_prov(base_path, nested=nested, single_tool=single_tool, directory=directory,
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224 secondary_files=secondary_files)
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225
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226 def check_folders(base_path):
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227 required_folders = [
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228 "data", "snapshot", "workflow", "metadata", os.path.join("metadata", "provenance")]
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229
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230 for folder in required_folders:
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231 assert os.path.isdir(os.path.join(base_path, folder))
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232
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233 def check_bagit(base_path):
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234 # check bagit structure
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235 required_files = [
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236 "bagit.txt", "bag-info.txt", "manifest-sha1.txt",
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237 "tagmanifest-sha1.txt", "tagmanifest-sha256.txt"]
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238
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239 for basename in required_files:
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240 file_path = os.path.join(base_path, basename)
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241 assert os.path.isfile(file_path)
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242
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243 bag = bagit.Bag(base_path)
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244 assert bag.has_oxum()
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245 (only_manifest, only_fs) = bag.compare_manifests_with_fs()
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246 assert not list(only_manifest), "Some files only in manifest"
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247 assert not list(only_fs), "Some files only on file system"
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248 missing_tagfiles = bag.missing_optional_tagfiles()
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249 assert not list(missing_tagfiles), "Some files only in tagmanifest"
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250 bag.validate()
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251 # TODO: Check other bag-info attributes
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252 assert arcp.is_arcp_uri(bag.info.get("External-Identifier"))
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253
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254 def find_arcp(base_path):
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255 # First try to find External-Identifier
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256 bag = bagit.Bag(base_path)
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257 ext_id = bag.info.get("External-Identifier")
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258 if arcp.is_arcp_uri(ext_id):
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259 return ext_id
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260 raise Exception("Can't find External-Identifier")
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261
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262 def _arcp2file(base_path, uri):
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263 parsed = arcp.parse_arcp(uri)
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264 # arcp URIs, ensure they are local to our RO
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265 assert parsed.uuid == arcp.parse_arcp(find_arcp(base_path)).uuid,\
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266 'arcp URI must be local to the research object'
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267
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268 path = parsed.path[1:] # Strip first /
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269 # Convert to local path, in case it uses \ on Windows
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270 lpath = str(Path(path))
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271 return os.path.join(base_path, lpath)
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272
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273 def check_ro(base_path, nested=False):
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274 manifest_file = os.path.join(base_path, "metadata", "manifest.json")
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275 assert os.path.isfile(manifest_file), "Can't find " + manifest_file
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276 arcp_root = find_arcp(base_path)
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277 base = urllib.parse.urljoin(arcp_root, "metadata/manifest.json")
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278 g = Graph()
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279
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280 # Avoid resolving JSON-LD context https://w3id.org/bundle/context
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281 # so this test works offline
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282 context = Path(get_data("tests/bundle-context.jsonld")).as_uri()
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283 with open(manifest_file, "r", encoding="UTF-8") as f:
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284 jsonld = f.read()
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285 # replace with file:/// URI
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286 jsonld = jsonld.replace("https://w3id.org/bundle/context", context)
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287 g.parse(data=jsonld, format="json-ld", publicID=base)
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288 if os.environ.get("DEBUG"):
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289 print("Parsed manifest:\n\n")
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290 g.serialize(sys.stdout, format="ttl")
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291 ro = None
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292
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293 for ro in g.subjects(ORE.isDescribedBy, URIRef(base)):
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294 break
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295 assert ro is not None, "Can't find RO with ore:isDescribedBy"
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296
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297 profile = None
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298 for dc in g.objects(ro, DCTERMS.conformsTo):
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299 profile = dc
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300 break
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301 assert profile is not None, "Can't find profile with dct:conformsTo"
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302 assert profile == URIRef(provenance.CWLPROV_VERSION),\
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303 "Unexpected cwlprov version " + profile
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304
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305 paths = []
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306 externals = []
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307 for aggregate in g.objects(ro, ORE.aggregates):
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308 if not arcp.is_arcp_uri(aggregate):
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309 externals.append(aggregate)
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310 # Won't check external URIs existence here
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311 # TODO: Check they are not relative!
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312 continue
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313 lfile = _arcp2file(base_path, aggregate)
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314 paths.append(os.path.relpath(lfile, base_path))
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315 assert os.path.isfile(lfile), "Can't find aggregated " + lfile
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316
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317 assert paths, "Didn't find any arcp aggregates"
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318 assert externals, "Didn't find any data URIs"
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319
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320 for ext in ["provn", "xml", "json", "jsonld", "nt", "ttl"]:
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321 f = "metadata/provenance/primary.cwlprov.%s" % ext
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322 assert f in paths, "provenance file missing " + f
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323
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324 for f in ["workflow/primary-job.json", "workflow/packed.cwl", "workflow/primary-output.json"]:
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325 assert f in paths, "workflow file missing " + f
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326 # Can't test snapshot/ files directly as their name varies
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327
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328 # TODO: check urn:hash::sha1 thingies
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329 # TODO: Check OA annotations
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330
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331 packed = urllib.parse.urljoin(arcp_root, "/workflow/packed.cwl")
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332 primary_job = urllib.parse.urljoin(arcp_root, "/workflow/primary-job.json")
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333 primary_prov_nt = urllib.parse.urljoin(arcp_root, "/metadata/provenance/primary.cwlprov.nt")
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334 uuid = arcp.parse_arcp(arcp_root).uuid
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335
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336 highlights = set(g.subjects(OA.motivatedBy, OA.highlighting))
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337 assert highlights, "Didn't find highlights"
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338 for h in highlights:
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339 assert (h, OA.hasTarget, URIRef(packed)) in g
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340
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341 describes = set(g.subjects(OA.motivatedBy, OA.describing))
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342 for d in describes:
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343 assert (d, OA.hasBody, URIRef(arcp_root)) in g
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344 assert (d, OA.hasTarget, URIRef(uuid.urn)) in g
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345
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346 linked = set(g.subjects(OA.motivatedBy, OA.linking))
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347 for l in linked:
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348 assert (l, OA.hasBody, URIRef(packed)) in g
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349 assert (l, OA.hasBody, URIRef(primary_job)) in g
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350 assert (l, OA.hasTarget, URIRef(uuid.urn)) in g
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351
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352 has_provenance = set(g.subjects(OA.hasBody, URIRef(primary_prov_nt)))
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353 for p in has_provenance:
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354 assert (p, OA.hasTarget, URIRef(uuid.urn)) in g
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355 assert (p, OA.motivatedBy, PROV.has_provenance) in g
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356 # Check all prov elements are listed
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357 formats = set()
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358 for prov in g.objects(p, OA.hasBody):
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359 assert (prov, DCTERMS.conformsTo, URIRef(provenance.CWLPROV_VERSION)) in g
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360 # NOTE: DC.format is a Namespace method and does not resolve like other terms
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361 formats.update(set(g.objects(prov, DC["format"])))
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362 assert formats, "Could not find media types"
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363 expected = set(Literal(f) for f in (
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364 "application/json",
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365 "application/ld+json",
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366 "application/n-triples",
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367 'text/provenance-notation; charset="UTF-8"',
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368 'text/turtle; charset="UTF-8"',
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369 "application/xml"
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370 ))
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371 assert formats == expected, "Did not match expected PROV media types"
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372
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373 if nested:
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374 # Check for additional PROVs
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diff changeset
375 # Let's try to find the other wf run ID
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parents:
diff changeset
376 otherRuns = set()
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parents:
diff changeset
377 for p in g.subjects(OA.motivatedBy, PROV.has_provenance):
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parents:
diff changeset
378 if (p, OA.hasTarget, URIRef(uuid.urn)) in g:
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guerler
parents:
diff changeset
379 continue
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diff changeset
380 otherRuns.update(set(g.objects(p, OA.hasTarget)))
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parents:
diff changeset
381 assert otherRuns, "Could not find nested workflow run prov annotations"
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parents:
diff changeset
382
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parents:
diff changeset
383 def check_prov(base_path, nested=False, single_tool=False, directory=False,
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parents:
diff changeset
384 secondary_files=False):
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diff changeset
385 prov_file = os.path.join(base_path, "metadata", "provenance", "primary.cwlprov.nt")
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parents:
diff changeset
386 assert os.path.isfile(prov_file), "Can't find " + prov_file
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diff changeset
387 arcp_root = find_arcp(base_path)
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parents:
diff changeset
388 # Note: We don't need to include metadata/provnance in base URI
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parents:
diff changeset
389 # as .nt always use absolute URIs
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diff changeset
390 g = Graph()
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diff changeset
391 with open(prov_file, "rb") as f:
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parents:
diff changeset
392 g.parse(file=f, format="nt", publicID=arcp_root)
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parents:
diff changeset
393 if os.environ.get("DEBUG"):
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diff changeset
394 print("Parsed %s:\n\n" % prov_file)
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parents:
diff changeset
395 g.serialize(sys.stdout, format="ttl")
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diff changeset
396 runs = set(g.subjects(RDF.type, WFPROV.WorkflowRun))
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diff changeset
397
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diff changeset
398 # master workflow run URI (as urn:uuid:) should correspond to arcp uuid part
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diff changeset
399 uuid = arcp.parse_arcp(arcp_root).uuid
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diff changeset
400 master_run = URIRef(uuid.urn)
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diff changeset
401 assert master_run in runs, "Can't find run %s in %s" % (master_run, runs)
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parents:
diff changeset
402 # TODO: we should not need to parse arcp, but follow
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parents:
diff changeset
403 # the has_provenance annotations in manifest.json instead
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parents:
diff changeset
404
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parents:
diff changeset
405 # run should have been started by a wf engine
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diff changeset
406
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diff changeset
407 engines = set(g.subjects(RDF.type, WFPROV.WorkflowEngine))
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parents:
diff changeset
408 assert engines, "Could not find WorkflowEngine"
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parents:
diff changeset
409 assert len(engines) == 1, "Found too many WorkflowEngines: %s" % engines
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diff changeset
410 engine = engines.pop()
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parents:
diff changeset
411
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parents:
diff changeset
412 assert (master_run, PROV.wasAssociatedWith, engine) in g, "Wf run not associated with wf engine"
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parents:
diff changeset
413 assert (engine, RDF.type, PROV.SoftwareAgent) in g, "Engine not declared as SoftwareAgent"
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parents:
diff changeset
414
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diff changeset
415 if single_tool:
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diff changeset
416 activities = set(g.subjects(RDF.type, PROV.Activity))
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parents:
diff changeset
417 assert len(activities) == 1, "Too many activities: %s" % activities
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diff changeset
418 # single tool exec, there should be no other activities
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diff changeset
419 # than the tool run
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diff changeset
420 # (NOTE: the WorkflowEngine is also activity, but not declared explicitly)
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diff changeset
421 else:
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diff changeset
422 # Check all process runs were started by the master worklow
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diff changeset
423 stepActivities = set(g.subjects(RDF.type, WFPROV.ProcessRun))
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diff changeset
424 # Although semantically a WorkflowEngine is also a ProcessRun,
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parents:
diff changeset
425 # we don't declare that,
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parents:
diff changeset
426 # thus only the step activities should be in this set.
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diff changeset
427 assert master_run not in stepActivities
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diff changeset
428 assert stepActivities, "No steps executed in workflow"
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diff changeset
429 for step in stepActivities:
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diff changeset
430 # Let's check it was started by the master_run. Unfortunately, unlike PROV-N
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parents:
diff changeset
431 # in PROV-O RDF we have to check through the n-ary qualifiedStart relation
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diff changeset
432 starts = set(g.objects(step, PROV.qualifiedStart))
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parents:
diff changeset
433 assert starts, "Could not find qualifiedStart of step %s" % step
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parents:
diff changeset
434 assert len(starts) == 1, "Too many qualifiedStart for step %s" % step
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parents:
diff changeset
435 start = starts.pop()
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diff changeset
436 assert (start, PROV.hadActivity, master_run) in g,\
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parents:
diff changeset
437 "Step activity not started by master activity"
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parents:
diff changeset
438 # Tip: Any nested workflow step executions should not be in this prov file,
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parents:
diff changeset
439 # but in separate file
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diff changeset
440 if nested:
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diff changeset
441 # Find some cwlprov.nt the nested workflow is described in
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parents:
diff changeset
442 prov_ids = set(g.objects(predicate=PROV.has_provenance))
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parents:
diff changeset
443 # FIXME: The above is a bit naive and does not check the subject is
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diff changeset
444 # one of the steps -- OK for now as this is the only case of prov:has_provenance
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diff changeset
445 assert prov_ids, "Could not find prov:has_provenance from nested workflow"
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parents:
diff changeset
446
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diff changeset
447 nt_uris = [uri for uri in prov_ids if uri.endswith("cwlprov.nt")]
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parents:
diff changeset
448 # TODO: Look up manifest conformsTo and content-type rather than assuming magic filename
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parents:
diff changeset
449 assert nt_uris, "Could not find *.cwlprov.nt"
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parents:
diff changeset
450 # Load into new graph
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parents:
diff changeset
451 g2 = Graph()
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parents:
diff changeset
452 nt_uri = nt_uris.pop()
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guerler
parents:
diff changeset
453 with open(_arcp2file(base_path, nt_uri), "rb") as f:
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parents:
diff changeset
454 g2.parse(file=f, format="nt", publicID=nt_uri)
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guerler
parents:
diff changeset
455 # TODO: Check g2 statements that it's the same UUID activity inside
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guerler
parents:
diff changeset
456 # as in the outer step
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guerler
parents:
diff changeset
457 if directory:
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parents:
diff changeset
458 directories = set(g.subjects(RDF.type, RO.Folder))
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guerler
parents:
diff changeset
459 assert directories
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guerler
parents:
diff changeset
460
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guerler
parents:
diff changeset
461 for d in directories:
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parents:
diff changeset
462 assert (d, RDF.type, PROV.Dictionary) in g
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parents:
diff changeset
463 assert (d, RDF.type, PROV.Collection) in g
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parents:
diff changeset
464 assert(d, RDF.type, PROV.Entity) in g
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guerler
parents:
diff changeset
465
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parents:
diff changeset
466 files = set()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
467 for entry in g.objects(d, PROV.hadDictionaryMember):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
468 assert (entry, RDF.type, PROV.KeyEntityPair) in g
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guerler
parents:
diff changeset
469 # We don't check what that filename is here
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parents:
diff changeset
470 assert set(g.objects(entry, PROV.pairKey))
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guerler
parents:
diff changeset
471
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guerler
parents:
diff changeset
472 # RO:Folder aspect
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parents:
diff changeset
473 assert set(g.objects(entry, RO.entryName))
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guerler
parents:
diff changeset
474 assert (d, ORE.aggregates, entry) in g
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guerler
parents:
diff changeset
475 assert (entry, RDF.type, RO.FolderEntry) in g
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parents:
diff changeset
476 assert (entry, RDF.type, ORE.Proxy) in g
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
477 assert (entry, ORE.proxyIn, d) in g
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
478 assert (entry, ORE.proxyIn, d) in g
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guerler
parents:
diff changeset
479
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guerler
parents:
diff changeset
480 # Which file?
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parents:
diff changeset
481 entities = set(g.objects(entry, PROV.pairEntity))
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guerler
parents:
diff changeset
482 assert entities
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parents:
diff changeset
483 f = entities.pop()
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guerler
parents:
diff changeset
484 files.add(f)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
485 assert (entry, ORE.proxyFor, f) in g
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
486 assert (f, RDF.type, PROV.Entity) in g
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guerler
parents:
diff changeset
487
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guerler
parents:
diff changeset
488 if not files:
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parents:
diff changeset
489 assert (d, RDF.type, PROV.EmptyCollection) in g
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guerler
parents:
diff changeset
490 assert (d, RDF.type, PROV.EmptyDictionary) in g
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guerler
parents:
diff changeset
491 if secondary_files:
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guerler
parents:
diff changeset
492 derivations = set(g.subjects(RDF.type, CWLPROV.SecondaryFile))
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guerler
parents:
diff changeset
493 assert derivations
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guerler
parents:
diff changeset
494 for der in derivations:
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guerler
parents:
diff changeset
495 sec = set(g.subjects(PROV.qualifiedDerivation, der)).pop()
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guerler
parents:
diff changeset
496 prim = set(g.objects(der, PROV.entity)).pop()
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guerler
parents:
diff changeset
497
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guerler
parents:
diff changeset
498 # UUID specializes a hash checksum
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parents:
diff changeset
499 assert set(g.objects(sec, PROV.specializationOf))
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guerler
parents:
diff changeset
500 # extensions etc.
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parents:
diff changeset
501 sec_basename = set(g.objects(sec, CWLPROV.basename)).pop()
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parents:
diff changeset
502 sec_nameroot = set(g.objects(sec, CWLPROV.nameroot)).pop()
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parents:
diff changeset
503 sec_nameext = set(g.objects(sec, CWLPROV.nameext)).pop()
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guerler
parents:
diff changeset
504 assert str(sec_basename) == "%s%s" % (sec_nameroot, sec_nameext)
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guerler
parents:
diff changeset
505 # TODO: Check hash data file exist in RO
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parents:
diff changeset
506
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parents:
diff changeset
507 # The primary entity should have the same, but different values
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parents:
diff changeset
508 assert set(g.objects(prim, PROV.specializationOf))
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parents:
diff changeset
509 prim_basename = set(g.objects(prim, CWLPROV.basename)).pop()
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guerler
parents:
diff changeset
510 prim_nameroot = set(g.objects(prim, CWLPROV.nameroot)).pop()
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parents:
diff changeset
511 prim_nameext = set(g.objects(prim, CWLPROV.nameext)).pop()
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parents:
diff changeset
512 assert str(prim_basename) == "%s%s" % (prim_nameroot, prim_nameext)
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parents:
diff changeset
513
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514
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diff changeset
515 @pytest.fixture
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diff changeset
516 def research_object():
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517 re_ob = provenance.ResearchObject(StdFsAccess(''))
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diff changeset
518 yield re_ob
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diff changeset
519 re_ob.close()
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diff changeset
520
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521 def test_absolute_path_fails(research_object):
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diff changeset
522 with pytest.raises(ValueError):
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523 research_object.write_bag_file("/absolute/path/fails")
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diff changeset
524
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diff changeset
525 def test_climboutfails(research_object):
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diff changeset
526 with pytest.raises(ValueError):
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diff changeset
527 research_object.write_bag_file("../../outside-ro")
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diff changeset
528
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diff changeset
529 def test_writable_string(research_object):
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diff changeset
530 with research_object.write_bag_file("file.txt") as file:
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guerler
parents:
diff changeset
531 assert file.writable()
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diff changeset
532 file.write(u"Hello\n")
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guerler
parents:
diff changeset
533 # TODO: Check Windows does not modify \n to \r\n here
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parents:
diff changeset
534
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diff changeset
535 sha1 = os.path.join(research_object.folder, "tagmanifest-sha1.txt")
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parents:
diff changeset
536 assert os.path.isfile(sha1)
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parents:
diff changeset
537
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parents:
diff changeset
538 with open(sha1, "r", encoding="UTF-8") as sha_file:
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parents:
diff changeset
539 stripped_sha = sha_file.readline().strip()
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parents:
diff changeset
540 assert stripped_sha.endswith("file.txt")
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parents:
diff changeset
541 #stain@biggie:~/src/cwltool$ echo Hello | sha1sum
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guerler
parents:
diff changeset
542 #1d229271928d3f9e2bb0375bd6ce5db6c6d348d9 -
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guerler
parents:
diff changeset
543 assert stripped_sha.startswith("1d229271928d3f9e2bb0375bd6ce5db6c6d348d9")
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parents:
diff changeset
544
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545 sha256 = os.path.join(research_object.folder, "tagmanifest-sha256.txt")
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parents:
diff changeset
546 assert os.path.isfile(sha256)
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diff changeset
547
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parents:
diff changeset
548 with open(sha256, "r", encoding="UTF-8") as sha_file:
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parents:
diff changeset
549 stripped_sha = sha_file.readline().strip()
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guerler
parents:
diff changeset
550
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diff changeset
551 assert stripped_sha.endswith("file.txt")
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diff changeset
552 #stain@biggie:~/src/cwltool$ echo Hello | sha256sum
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diff changeset
553 #66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18 -
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parents:
diff changeset
554 assert stripped_sha.startswith("66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18")
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guerler
parents:
diff changeset
555
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556 sha512 = os.path.join(research_object.folder, "tagmanifest-sha512.txt")
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parents:
diff changeset
557 assert os.path.isfile(sha512)
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diff changeset
558
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diff changeset
559 def test_writable_unicode_string(research_object):
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diff changeset
560 with research_object.write_bag_file("file.txt") as file:
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parents:
diff changeset
561 assert file.writable()
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562 file.write(u"Here is a snowman: \u2603 \n")
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guerler
parents:
diff changeset
563
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parents:
diff changeset
564 def test_writable_bytes(research_object):
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parents:
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565 string = u"Here is a snowman: \u2603 \n".encode("UTF-8")
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parents:
diff changeset
566 with research_object.write_bag_file("file.txt", encoding=None) as file:
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parents:
diff changeset
567 file.write(string)
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parents:
diff changeset
568
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
569 def test_data(research_object):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
570 with research_object.write_bag_file("data/file.txt") as file:
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parents:
diff changeset
571 assert file.writable()
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parents:
diff changeset
572 file.write(u"Hello\n")
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
573 # TODO: Check Windows does not modify \n to \r\n here
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guerler
parents:
diff changeset
574
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
575 # Because this is under data/ it should add to manifest
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
576 # rather than tagmanifest
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diff changeset
577 sha1 = os.path.join(research_object.folder, "manifest-sha1.txt")
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guerler
parents:
diff changeset
578 assert os.path.isfile(sha1)
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parents:
diff changeset
579 with open(sha1, "r", encoding="UTF-8") as file:
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parents:
diff changeset
580 stripped_sha = file.readline().strip()
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guerler
parents:
diff changeset
581 assert stripped_sha.endswith("data/file.txt")
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diff changeset
582
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diff changeset
583 def test_not_seekable(research_object):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
584 with research_object.write_bag_file("file.txt") as file:
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guerler
parents:
diff changeset
585 assert not file.seekable()
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parents:
diff changeset
586 with pytest.raises(IOError):
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parents:
diff changeset
587 file.seek(0)
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parents:
diff changeset
588
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parents:
diff changeset
589 def test_not_readable(research_object):
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parents:
diff changeset
590 with research_object.write_bag_file("file.txt") as file:
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guerler
parents:
diff changeset
591 assert not file.readable()
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parents:
diff changeset
592 with pytest.raises(IOError):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
593 file.read()
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guerler
parents:
diff changeset
594
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parents:
diff changeset
595 def test_truncate_fails(research_object):
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diff changeset
596 with research_object.write_bag_file("file.txt") as file:
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guerler
parents:
diff changeset
597 file.write(u"Hello there")
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parents:
diff changeset
598 file.truncate() # OK as we're always at end
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guerler
parents:
diff changeset
599 # Will fail because the checksum can't rewind
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parents:
diff changeset
600 with pytest.raises(IOError):
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guerler
parents:
diff changeset
601 file.truncate(0)
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guerler
parents:
diff changeset
602
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guerler
parents:
diff changeset
603
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guerler
parents:
diff changeset
604 mod_validness = [
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
605 # Taken from "Some sample ORCID iDs" on
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
606 # https://support.orcid.org/knowledgebase/articles/116780-structure-of-the-orcid-identifier
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
607 ("0000-0002-1825-0097", True),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
608 ("0000-0001-5109-3700", True),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
609 ("0000-0002-1694-233X", True),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
610 # dashes optional
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
611 ("0000000218250097", True),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
612 ("0000000151093700", True),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
613 ("000000021694233X", True),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
614 # do not fail on missing digits
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
615 ("0002-1694-233X", True),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
616 # Swap check-digits around to force error
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
617 ("0000-0002-1825-009X", False),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
618 ("0000-0001-5109-3707", False),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
619 ("0000-0002-1694-2330", False)
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guerler
parents:
diff changeset
620 ]
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guerler
parents:
diff changeset
621
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guerler
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622 @pytest.mark.parametrize('mod11,valid', mod_validness)
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623 def test_check_mod_11_2(mod11, valid):
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624 assert provenance._check_mod_11_2(mod11) == valid
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625
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626
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627 orcid_uris = [
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628 # https://orcid.org/ (Expected form)
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629 ("https://orcid.org/0000-0002-1694-233X", "https://orcid.org/0000-0002-1694-233X"),
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630 # orcid.org
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631 ("http://orcid.org/0000-0002-1694-233X", "https://orcid.org/0000-0002-1694-233X"),
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632 # just the number
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633 ("0000-0002-1825-0097", "https://orcid.org/0000-0002-1825-0097"),
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634 # lower-case X is OK (and fixed)
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635 ("https://orcid.org/0000-0002-1694-233x", "https://orcid.org/0000-0002-1694-233X"),
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636 # upper-case ORCID.ORG is OK.. (and fixed)
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637 ("https://ORCID.ORG/0000-0002-1694-233X", "https://orcid.org/0000-0002-1694-233X"),
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638 # Unicode string (Python 2)
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639 (u"https://orcid.org/0000-0002-1694-233X", "https://orcid.org/0000-0002-1694-233X")
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640 ]
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641
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642 @pytest.mark.parametrize('orcid,expected', orcid_uris)
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643 def test_valid_orcid(orcid, expected):
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644 assert provenance._valid_orcid(orcid) == expected
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645
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646
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647 invalid_orcids = [
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648 # missing digit fails (even if checksum is correct)
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649 "0002-1694-2332",
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650 # Wrong checkdigit fails
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651 "https://orcid.org/0000-0002-1694-2332",
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652 "0000-0002-1694-2332",
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653 # Missing dashes fails (although that's OK for checksum)
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654 "https://orcid.org/000000021694233X",
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655 "000000021694233X",
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656 # Wrong hostname fails
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657 "https://example.org/0000-0002-1694-233X",
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658 # Wrong protocol fails
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659 "ftp://orcid.org/0000-0002-1694-233X",
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660 # Trying to be clever fails (no URL parsing!)
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661 "https://orcid.org:443/0000-0002-1694-233X",
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662 "http://orcid.org:80/0000-0002-1694-233X",
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663 # Empty string is not really valid
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664 ""
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665 ]
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666
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667 @pytest.mark.parametrize('orcid', invalid_orcids)
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668 def test_invalid_orcid(orcid):
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669 with pytest.raises(ValueError):
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670 provenance._valid_orcid(orcid)
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671
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672 def test_whoami():
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673 username, fullname = provenance._whoami()
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674 assert username and isinstance(username, str)
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675 assert fullname and isinstance(fullname, str)
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676
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677 def test_research_object():
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678 # TODO: Test ResearchObject methods
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679 pass
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680
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681 # Reasearch object may need to be pickled (for Toil)
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682 def test_research_object_picklability(research_object):
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683 assert pickle.dumps(research_object) is not None